{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8557UXEJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8557UXEJ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8557UXEJ](/auxiliary-sets/IGVFDS8557UXEJ/) has sequence file(s) [IGVFFI3665MLGM](/sequence-files/IGVFFI3665MLGM/), [IGVFFI2578WMMF](/sequence-files/IGVFFI2578WMMF/), [IGVFFI1790WPVC](/sequence-files/IGVFFI1790WPVC/), [IGVFFI3467MIOR](/sequence-files/IGVFFI3467MIOR/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8557UXEJ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8557UXEJ](/auxiliary-sets/IGVFDS8557UXEJ/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS8557UXEJ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-14T16:24:18.255872+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3665MLGM/",
"accession": "IGVFFI3665MLGM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:06.950336+00:00",
"file_format": "fastq",
"file_size": 26786723,
"href": "/sequence-files/IGVFFI3665MLGM/@@download/IGVFFI3665MLGM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ac82b965-f1a5-4fd2-a996-cd9f362d7083/IGVFFI3665MLGM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR1-Rep1_S121_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6081UZGH/",
"accession": "IGVFFI6081UZGH",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:42:46.451287+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI6081UZGH/@@download/IGVFFI6081UZGH.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b5058077-69f4-46a8-8635-f7cbb7903976/IGVFFI6081UZGH.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2578WMMF/",
"accession": "IGVFFI2578WMMF",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:25.066769+00:00",
"file_format": "fastq",
"file_size": 33392181,
"href": "/sequence-files/IGVFFI2578WMMF/@@download/IGVFFI2578WMMF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5bc419ed-8f8a-4561-ac19-7a6ec211cc9a/IGVFFI2578WMMF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR2-Rep1_S127_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1790WPVC/",
"accession": "IGVFFI1790WPVC",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:52:43.108337+00:00",
"file_format": "fastq",
"file_size": 29186941,
"href": "/sequence-files/IGVFFI1790WPVC/@@download/IGVFFI1790WPVC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/beefd2e9-4fba-4d73-9a37-cf23e8e5f6e9/IGVFFI1790WPVC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR3-Rep1_S175_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3467MIOR/",
"accession": "IGVFFI3467MIOR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T01:53:01.391441+00:00",
"file_format": "fastq",
"file_size": 45919416,
"href": "/sequence-files/IGVFFI3467MIOR/@@download/IGVFFI3467MIOR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/9ea2cfd3-e629-4a44-afaa-2dc1906cfcd2/IGVFFI3467MIOR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR4-Rep1_S181_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9888WBKI/",
"accession": "IGVFFI9888WBKI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:00.223195+00:00",
"file_format": "yaml",
"file_size": 914,
"href": "/configuration-files/IGVFFI9888WBKI/@@download/IGVFFI9888WBKI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/f2cfbda7-8baa-4d3e-be49-d0419960fa82/IGVFFI9888WBKI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9150PTBN/",
"accession": "IGVFFI9150PTBN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:27.814614+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI9150PTBN/@@download/IGVFFI9150PTBN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/b782090b-a56d-4e21-9ca3-d210484484e3/IGVFFI9150PTBN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8784VUEB/",
"accession": "IGVFFI8784VUEB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:43:13.648745+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI8784VUEB/@@download/IGVFFI8784VUEB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/cb07ef55-8bd8-4c61-9a66-2784d08095a3/IGVFFI8784VUEB.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0101WKZK/",
"accession": "IGVFDS0101WKZK",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:11:22.474625+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1718NCDJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1718NCDJ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1891GTLU/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of FAM3C) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:52:06.950336+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e7b5eb9e-7e1b-4ac3-a021-07306fe11297"
}